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Viral bioinformatics: Dotplot

Dotplots are an extremely useful way of visualizing comparisons of small and large DNA sequences (as well as protein sequences), providing insight into the degree of similarity, deletions, insertions and direct and indirect repeats. In a dotplot, each nucleotide, or small window of nucleotides, of one sequence is compared with every nucleotide of a second sequence. Dotplots can quickly provide an overview of the relationship between sequences.